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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttatttcaagacatgtttcaatccttttaataggtgttcctgtttcgaatttaatgtcagctggctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA

Basic information

species Oryza sativa
transcript LOC_Os09g34040.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G142806_T01 (Zea mays), 3'ss of exon 5
--------gtgagcttatttcaaga-catgtttcaatccttttaataggtgttcctgt-ttcgaatttaatgtcagctggctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA
         ||||    | | |||| ||| |  |     ||  | | |  ||| || | || ||||||||| | ||||||||||||||||||||||| ||||||  ||||||| ||||||||||||| || |||||||| || |||||||| ||||||||||||||||||||||||||||| ||||
gtgagtagttgagaaggtgtaaagatcatatagcttattttgaatttgccgtttctatatttgaatttaatat-agctggctacagGGATATGCACCGCCTAATAAAGATAGACGAGAAGGTGTTCTAACAAGGAAAAGGCTGGAGTACGTGGAATGTGTTTCTCAATACTATGATATTCCAGATA

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G13330.2 (Glycine max), 3'ss of exon 4
----------------gtgagc-ttatt---tca-agacatgtttcaatccttttaataggtgttcctgtttc---gaatttaatgtca-gctggctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA
                || | | |||||    || || || || |   |  | |  ||||   ||  | || |    ||||||| |  |  ||| | |||||||||||||||||||||| |||||||||| || || ||||| |  |||||  | ||||||||  |||| ||| ||||||| || ||||||||||||||||
atcattttagtaaggggtcaacattattgacccacagtcacgtgt-gtttttatggatagcattttgtcttcctggaaatttaaagatatactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGGAGTTCTAAGAAGGAAGCGCCTTGAGTATCTTGACTGTATTTCTCAGTATTATGATATTCCTGATA

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G03200.1 (Glycine max), 3'ss of exon 4
---------gtgagcttatttcaagaca-----tgtttcaatc-----cttttaataggtgttcctgtttcgaatttaatgtcagctgg-----ctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA
          | | ||| ||| ||   |     |   | ||||      |||  || | |  |    ||||  ||| ||  |  | ||      | |||||||||||||||||||||| |||||||||| || || ||| |||  |||||  | ||||||||  |||| ||||||||||| || ||||||||||||||||
accctatagataatctttttttaaagtaataagtaggttaatcacatgttttctatggatactttcttttcttattaaaaatttgatgaaatgtcaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGGAGTTTTGAAAAGGAAGCGCCTTGAGTATCTTGACTGTGTTTCTCAGTATTATGATATTCCTGATA

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G05350.1 (Glycine max), 3'ss of exon 4
----------------gtgagc-ttatttcaagacatgtttcaatccttttaataggtgt--tcctgtttc-----gaatttaatgtca-gctggctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA
                || | | |||||     ||| ||| ||    |||| || |||    |  ||| |       ||||||| |  |  ||| | |||||||||||||||||||||| |||||||||| || || ||||| |  |||||| | ||||||||  |||| ||| ||||||| || ||||||||||||||||
attatttgagtaaggggtcaacattattgacccaca-gttacatgtgtttttatgggtagcattttgtcttcctggaaatttaaagatatactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGGAGTTCTAAGAAGGAAACGCCTTGAGTATCTTGACTGTATTTCTCAGTATTATGATATTCCTGATA

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G42180.1 (Glycine max), 3'ss of exon 4
--------gtgagcttatttc------aagacatgtttcaatc-----cttttaataggtgttcctgtttcgaatttaatgtc-----agctggctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA
         | | ||| |||       || | ||   | ||||      |||  || | |  |    ||||  ||| ||  |      | ||||| |||||||||||||||||||||| |||||||||| || || ||| |||  |||||  | ||||||||  |||| ||||||||||| || ||||||||||||||||
ccctatagataatcttttttttaaagtaataaataggttaatcacatgttttctatggatactttcttttcttattaaaaatttaatgaactggcaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGGAGTTTTGAAAAGGAAGCGCCTTGAGTATCTTGACTGTGTTTCTCAGTATTATGATATTCCTGATA

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------gtgagcttatttcaa-gacatgt------ttcaatccttttaataggtgttcctgtttcgaatttaatgtcagctggctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA
                  | ||||  || ||   ||| |       ||      |||   | | | |  || |||  | || ||| | | ||| | |||||||||||||||||||||| |||||||||| || | ||||||||  || ||| | ||||| ||  | |||| ||||   ||||  |||||  |||| ||| 
gtcagatgatttgtgttattagctctttccatcaacacggcaactattttggattttggtttgttatgtctatttgaatttaaatataaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGCTGTTCTGAGAAGAAAACGTCTTGAATATCTGGAATCTGTTGGCCAATTTTATGACCTTCCAGATT

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtgagcttatttcaagacatgtttcaatcctttta-ataggtgttcctgtttcgaatttaa-tgtcagctggctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA
                       ||  ||  | | || |    ||   ||     || ||  || |   || ||  | ||||| | | | ||| | |||||||||||||||||||||| |||||||||| || ||||||||||  |||||  | ||||||||  |||| ||||||||||| || ||||| ||||| || |
tctgagtacaagcatacctagtatggtctcttattaacagtgattgttattggactatatctgtttgtttggttgaagtttaaatatgaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGGTGTTCTGAAAAGGAAGCGCCTTGAGTATCTTGACTGTGTTTCTCAGTATTATGACATTCCAGACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 51 (upstream exon), 74 (downstream exon)
Score: 26

ACAAGTTGCGGGAACTGTCTTGGAGTGGTGTTCCACCTTATATGCGACCTAATATATGGAGACTTCTTCTGgtgagcttat ... ctggctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaatccttttaataggtgttcctgtttcgaatttaatgtcagctggctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA
                                aatttaatgt  TA-rich tract